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- PDB-1gv0: Structural Basis for Thermophilic Protein Stability: Structures o... -

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Basic information

Entry
Database: PDB / ID: 1gv0
TitleStructural Basis for Thermophilic Protein Stability: Structures of Thermophilic and Mesophilic Malate Dehydrogenases
ComponentsMALATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / DEHYDROGENASE / TRICARBOXYLIC ACID / NAD
Function / homology
Function and homology information


malate dehydrogenase / L-malate dehydrogenase activity / carboxylic acid metabolic process / tricarboxylic acid cycle
Similarity search - Function
Malate dehydrogenase, type 3 / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / L-lactate/malate dehydrogenase / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / NAD(P)-binding Rossmann-like Domain ...Malate dehydrogenase, type 3 / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / L-lactate/malate dehydrogenase / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Malate dehydrogenase
Similarity search - Component
Biological speciesCHLOROBIUM TEPIDUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDalhus, B. / Sarinen, M. / Sauer, U.H. / Eklund, P. / Johansson, K. / Karlsson, A. / Ramaswamy, S. / Bjork, A. / Synstad, B. / Naterstad, K. ...Dalhus, B. / Sarinen, M. / Sauer, U.H. / Eklund, P. / Johansson, K. / Karlsson, A. / Ramaswamy, S. / Bjork, A. / Synstad, B. / Naterstad, K. / Sirevag, R. / Eklund, H.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Structural Basis for Thermophilic Protein Stability: Structures of Thermophilic and Mesophilic Malate Dehydrogenases
Authors: Dalhus, B. / Saarinen, M. / Sauer, U.H. / Eklund, P. / Johansson, K. / Karlsson, A. / Ramaswamy, S. / Bjork, A. / Synstad, B. / Naterstad, K. / Sirevag, R. / Eklund, H.
History
DepositionFeb 4, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jan 17, 2018Group: Atomic model / Data collection / Category: atom_site / diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MALATE DEHYDROGENASE
B: MALATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,6154
Polymers66,2882
Non-polymers1,3272
Water4,197233
1
A: MALATE DEHYDROGENASE
B: MALATE DEHYDROGENASE
hetero molecules

A: MALATE DEHYDROGENASE
B: MALATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,2318
Polymers132,5774
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+3/21
MethodPQS
Unit cell
Length a, b, c (Å)114.320, 149.420, 97.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein MALATE DEHYDROGENASE /


Mass: 33144.230 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CHLOROBIUM TEPIDUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P80039, malate dehydrogenase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60 %
Crystal growpH: 7.5
Details: 20MG/ML,50MMTRIS-HCL,PH7.4,55%MPD, 100MMHEPES,PH7.5., pH 7.50
Crystal grow
*PLUS
Temperature: 15 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
250 mMTris-HCl1droppH7.4
353 %(v/v)MPD1reservoir
4100 mMHEPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.9831
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9831 Å / Relative weight: 1
ReflectionResolution: 2.5→40.8 Å / Num. obs: 28459 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 14.5 Å2 / Rmerge(I) obs: 0.07
Reflection shellResolution: 2.5→2.64 Å / Rmerge(I) obs: 0.254 / % possible all: 100
Reflection
*PLUS
% possible obs: 100 % / Num. measured all: 117908 / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MDH WITH PDB-CODE 1GUZ

1guz


Resolution: 2.5→40.9 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3775346.2 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.275 2823 9.9 %RANDOM
Rwork0.221 ---
obs0.221 28459 97.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.952 Å2 / ksol: 0.371756 e/Å3
Displacement parametersBiso mean: 32.8 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.5→40.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4451 0 88 233 4772
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.351.5
X-RAY DIFFRACTIONc_mcangle_it2.222
X-RAY DIFFRACTIONc_scbond_it1.942
X-RAY DIFFRACTIONc_scangle_it2.882.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.373 437 10.2 %
Rwork0.311 3830 -
obs--88.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 31.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.15
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83

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